In China, geographical indications (GIs) are seen as certificates or collective trademarks, as well as representations of quality agricultural products, and are important in revitalizing the countryside. Therefore, a combined qualitative and quantitative method was employed to examine the operational practices of GIs at the relatively micro-level of the municipality in order to identify their effectiveness and challenges in rural revitalization and propose more targeted optimization suggestions. Pengshui Miao and Tujia Autonomous County, located in the Wuling Mountains in southeastern Chongqing, is an excellent example of the positive impact GIs can have on rural development, boasting the highest number of GI trademarks in the region. Despite the large number of GIs in Pengshui, there are several issues that need to be addressed, including low brand awareness, lack of product enhancement, and poor market competitiveness. To overcome these challenges, there must be a shift from a quantity-based to a quality-based approach to GI trademark declarations. This requires promoting the transformation of traditional agriculture into modern agriculture, investing in rural infrastructure, and improving the efficiency and quality of GI product production. By doing so, individuals in the local community will be able to reap the benefits of GI trademarks, improving their income and standard of living. In view of the fact that administrative divisions and cultural regions overlap, it is important to promote interregional cooperation and encourage declarations of GI trademarks in neighboring counties. This will help to preserve the area’s local cultural heritage and promote its heritage through GIs. By taking a targeted approach to GI trademark declarations and promoting cooperation between regions, Pengshui, and other rural communities can maximize the benefits of GIs and support sustainable rural development.